crlmm-package | Genotype Calling via CRLMM Algorithm |
ABpanel | A panel function for plotting prediction regions and log-normalized intensities |
BafLrrSetList | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~ |
BafLrrSetList-method | crlmm methods for class "CNSet" |
CA | Accessors for allele-specific or total copy number |
CA-method | crlmm methods for class "CNSet" |
calculateRBaf | Calculate log R ratios and B allele frequencies. |
calculateRBaf-method | Calculate log R ratios and B allele frequencies. |
CB | Accessors for allele-specific or total copy number |
CB-method | crlmm methods for class "CNSet" |
celDates | Reads cel files and return an error if a file is not read |
cnrmaAffy | quantile normalize nonpolymorphic markers |
cnSetExample | Object of class 'CNSet' |
cnSetExample2 | Object of class 'CNSet' |
coerce-method | crlmm methods for class "CNSet" |
constructAffyCNSet | Construct an object of class CNSet from Affymetrix cel files |
constructInf | Instantiate an object of class CNSet for the Infinium platforms. |
corr | Accessors for batch-specific summary statistics. |
corr-method | Methods for class "AssayData" in crlmm |
corr-method | crlmm methods for class "CNSet" |
crlmm | Genotype oligonucleotide arrays with CRLMM |
crlmm2 | Genotype oligonucleotide arrays with CRLMM |
crlmmCopynumber | Locus- and allele-specific estimation of copy number |
crlmmCopynumber2 | Locus- and allele-specific estimation of copy number |
crlmmCopynumberLD | Locus- and allele-specific estimation of copy number |
crlmmIllumina | Preprocessing and genotyping of Illumina Infinium II arrays. |
genotype | Preprocessing and genotyping of Affymetrix arrays. |
genotype.Illumina | Preprocessing and genotyping of Illumina Infinium II arrays. |
genotype2 | Preprocessing and genotyping of Affymetrix arrays. |
genotypeAffy | Genotype Affymetrix CEL files |
genotypeInf | Genotyping of Illumina Infinium II arrays. |
genotypeLD | Preprocessing and genotyping of Affymetrix arrays. |
genotypes | The possible genotypes for an integer copy number. |
lines-method | crlmm methods for class "CNSet" |
mads | Accessors for batch-specific summary statistics. |
mads-method | Methods for class "AssayData" in crlmm |
mads-method | crlmm methods for class "CNSet" |
medians | Accessors for batch-specific summary statistics. |
medians-method | Methods for class "AssayData" in crlmm |
medians-method | crlmm methods for class "CNSet" |
Ns | Accessors for batch-specific summary statistics. |
Ns-method | Methods for class "AssayData" in crlmm |
Ns-method | crlmm methods for class "CNSet" |
nuA | Accessors for allele-specific or total copy number |
nuA-method | crlmm methods for class "CNSet" |
nuB | Accessors for allele-specific or total copy number |
nuB-method | crlmm methods for class "CNSet" |
OligoSetList | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~ |
OligoSetList-method | crlmm methods for class "CNSet" |
phiA | Accessors for allele-specific or total copy number |
phiA-method | crlmm methods for class "CNSet" |
phiB | Accessors for allele-specific or total copy number |
phiB-method | crlmm methods for class "CNSet" |
plotSamples | Make M vs S plot for SNPs or samples. |
plotSNPs | Make M vs S plot for SNPs or samples. |
posteriorProbability | Calculate the posterior probability for integer copy numbers. |
posteriorProbability-method | Calculate the posterior probability for integer copy numbers. |
predictionRegion | Prediction regions for integer copy number |
PredictionRegion-class | Class '"PredictionRegion"' |
predictionRegion-method | Prediction regions for integer copy number |
preprocessInf | Preprocessing of Illumina Infinium II arrays. |
rawCopynumber | Accessors for allele-specific or total copy number |
rawCopynumber-method | crlmm methods for class "CNSet" |
readGenCallOutput | Read X and Y intensities from GenCall output |
readIdatFiles | Reads Idat Files from Infinium II Illumina BeadChips |
readIdatFiles2 | Reads Idat Files from Infinium II Illumina BeadChips |
snprma | Preprocessing tool for SNP arrays. |
snprma2 | Preprocessing tool for SNP arrays. |
snprmaAffy | Quantile normalize intensities for SNPs |
tau2 | Accessors for batch-specific summary statistics. |
tau2-method | Methods for class "AssayData" in crlmm |
tau2-method | crlmm methods for class "CNSet" |
totalCopynumber | Accessors for allele-specific or total copy number |
totalCopynumber-method | crlmm methods for class "CNSet" |
validCdfNames | Supported annotation packages for crlmm genotyping |
validCEL | Reads cel files and return an error if a file is not read |
xyplot | Plot prediction regions and normalized intensities. |
xyplot-method | Plot prediction regions and normalized intensities. |
[-method | Class '"PredictionRegion"' |